A research and development project aimed at development of high content multiplex assays capable of simultaneous detection of 35 NIAID Category A, B, and C viral agents plus quantification of cytokine/chemokine responses in patients is proposed. Lawrence Livermore National Laboratory (LLNL), NanoString Technologies Corp. (NT), the University of Texas Medical Branch, and the University of California San Francisco propose to develop a molecular detection assay that will simultaneously detect the presence of any of 35 Category A, B, or C viruses in a patient sample and determine the disease state of the patient. The system envisioned will take advantage of LLNL's bioinformatics and viral assay development capabilities as well as NT's novel platform enabling direct quantification of nucleic acid molecules in clinically relevant samples. The assay will require minimal sample preparation with no need for amplification or enzymatic reactions. An integrated, quantitative, highly specific and sensitive [1 copy per cell] assay system with automated data analysis & output, requiring less than 20 minutes of hands-on manipulation and minimal sample preparation is envisioned. The system will allow simultaneous and sensitive multiplex detection of up to 700 analytes per sample. Initial throughput of up to 72 samples per instrument per 24 hour period is envisioned. The system will enable rapid modifications to the nucleic acid detection codesets such that the system can integrate new diagnostic tests for other agents (modified agents, high priority agents or others) and other host response genes. Finally, the system envisioned will require minimal operator training and expertise.